I did a little fixup in Gimp to show how the periods and ellipses should appear (though actually the ellipses I see in manga are three dots in the space of one character: this: … (but centered) rather than this: ・・・)

In vertical text, the period and comma are placed in the top right corner of the kanji box, rather than the bottom left corner.

The only manga I own in Japanese, 史上最強の弟子ケンイチ, uses 。 and 、at least sometimes (though !, !!, !? and ellipses are far more common ways to end sentences.) Checking the sample chapters at http://websunday.net, Detective Conan didn't seem to have any 。 and only a few 、, but a couple of other manga I checked had occasional 。 in them.